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Start Your TrialThis interface is used from the REST API to configure IQTREE runs, using the new Expanse cluster.
The Tool ID this interface is toolid=IQTREE_XSEDE_EXPANSE; other versions will be deprecated in June, 2021.
This tool allows use of up to 128 cores on the Expanse machine. This can be helpful.
However, performance on partitioned files can be poor. This interface allows you to configure runs with partitioned input files
to capture more memory. But this option should only be used when more memory is required for the run to succeed.
Supported parameters:
Input files:
input.infile_ - Primary Input File (named infile.txt by the app.)
input.specify_quartetset_ - NEXUS file specifying taxon clusters (-lmclust)
input.partition_file_ - Partition file
input.specify_nexusmodelfile_ - Specify a Nexus Model file. (-mdef)
input_guide_tree_ - Specify a guide tree file for PMSF analysis (-ft)
input_frequency_file_ - Specify a frequency file for PMSF analysis (-fs)
input.starting_tree_ - Specify a starting tree
input.constraint_file_ - Specify a topological constraint tree file in NEWICK format (-g)
input.specify_treefile_ - Specify a file containing a set of trees. (-z)
input.fixed_usertree_ - Specify a fixed user tree to estimate model parameters. (-te)
input.specify_ancestraltree_ - Specify a user-defined tree to determine ancestral sequences (-te)
input.tree_file1_ - Specify a file containing a set of trees (For consensus trees.)
input.target_treefile_ - Specify an input “target” tree file (-sup); no default.
input.tree_file2_ - Specify a second tree file for Robinsons Foulds calculations.
input.datatype2_file_ - Select the file with your second datatype (partition_datatype5.phy)
input.datatype3_file_ - Select the file with your third datatype (partition_datatype5.phy)
input.datatype4_file_ - Select the file with your fourth datatype (partition_datatype5.phy)
input.datatype5_file_ - Select the file with your fifth datatype (partition_datatype5.phy)
input.partition_modelfile2_ - Choose file that specifies the model selection (-S)
input.partition_tfile_ - Choose a reference tree file (coalescent/reconciliation approach) for gCF (-t)
input.setoftrees_file_ - Choose a set of trees for gCF (-gcf)
Visible Parameters:
vparam.runtime_ - (Float) - Maximum Hours to Run (up to 168 hours) default=0.5
vparam.which_iqtree_ - (Integer) - default is curent verrsion, 2.3.6 (=236); also 1.6.2 (=16). or 2.1.2 (=212) 2.3.2 (=232) are available.
vparam.more_memory_ - (Switch) - Use this when a partitioned run has failed due to lack of memory. Only available when a partion file is provided.
vparam.more_memory2_ - (Switch) - Only when more_memory = 0. This gives a whole node. Pricey, but sometimes needed.
vparam.specify_numpatterns_ - (Integer) - Specify the number of patterns in your input dataset. You can get this from out put of a quick preliminary run. Or just use the number of characters.
vparam.specify_safe_ - (Switch) - Use safe likelihood kernel to avoid numerical underflow (-safe)
vparam.datatype_ - (Excl) - Specify sequence type (-st); DNA; PROTEIN; BINARY; MORPH; CODON; NT2AA (default = DNA). Not allowed with mixed_sequence option in v 1.01.
vparam.codon_type_ - (Excl) - Specify Codon type; CODON1; CODON2; CODON3; CODON4; CODON5; CODON6; CODON9; CODON10; CODON11; CODON12; CODON13<; CODON14; CODON16; CODON21; CODON22; CODON23; CODON24; CODON25 (Default=CODON1)
vparam.nt2aa_type_ - (Excl) - Specify translation table; NT2AA1; NT2AA2; NT2AA3; NT2AA4; NT2AA5; NT2AA6; NT2AA9; NT2AA10; NT2AA11; NT2AA12; NT2AA13; NT2AA14; NT2AA16; NT2AA21; NT2AA22; NT2AA23; NT2AA24; NT2AA25; (default=NT2AA1)
vparam.use_nj_ - (Switch) - Use a NJ starting tree (-t BIONJ); no default.
vparam.use_random_ - (Switch) - Use a Random starting tree (-t RANDOM); no default.
vparam.specify_outgroup_ - (String) - Specify an outgroup (-o); no default.
vparam.specify_prefix_ - (String) - Specify the prefix for output files (-pre); no default.
vparam.specify_seed_ - (Integer) - Specify a seed for the run (-seed); no default.
Quartet Options
vparam.specify_quartets_ - (Excl) - Quartets to be randomly drawn (-lmap); ALL; specify_quartets; no default.
vparam.specify_quartetnum_ - (Integer) - Specify number of quartets; when specify_quartets_ = specify_quartets (no default)
vparam.write_quartets_ - (Switch) - Write quartets to a file.
vparam.specify_numparsquartets_ - (Integer) Specify number of parsimony-based sCF quartets (--scf)
vparam.specify_numlikquartets_ - (Integer) Specify number of likelihood-based ssCF quartets (--scfl)
Partition Options
vparam.nexus_partition_file_ - (Switch) My partitions are specified in a Nexus file.
vparam.partition_type_ - (Excl) - Specify partition type; -q; -spp; -sp; no default.
vparam.mixed_sequence_ - (Switch) - v 1.00.01+; I want to use multiple alignment files for a partitioned analysis
vparam.num_mixedsequences_ - (Excl) - v 1.00.01+ How many alignment files in your partitioned analysis (allowed 2, 3, 4, 5) no default
Automatic Model Selection Parameters
vparam.specify_model_ - (Excl) - Test for the best model (-m TEST); TESTONLY; TEST; TESTNEWONLY; TESTNEW; TESTMERGEONLY; TESTMERGE; TESTNEWMERGEONLY; TESTNEWMERGEONLY; TESTNEWMERGE; no default.
vparam.specify_liemarkov_ - (Excl) - Specify a Lie Markov Option, allowed values: +LM; +LMRY;+LMWS;+LMMK;+LMSS
vparam.select_rcluster_ - (Excl) - Specify the relaxed clustering algorithm to use (-rcluster); allowed values: -rcluster, rclusterf, rcluster-max
vparam.specify_rclusterval_ - (Integer) - Specify the percentage for relaxed clustering algorithm (-rcluster); no default.
vparam.specify_basemodels_ - (String) - Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program. Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations; (no default).
vparam.specify_aamodels_ - (Excl) - Specify nuclear, mitochondrial, chloroplast or viral (-msub, protein); nuclear, mitochondrial, chloroplast, viral; no default.write
vparam.specify_freqtypes_ - (String) - Specify a comma-separated list of frequency types for model selection (-mfreq) no default.
vparam.specify_ratehettypes_ - (String) Specify a comma-separated list of rate heterogeneity types for model selection (-mrate); no default.
vparam.specify_mincat_ - (Integer) - Specify minimum number of categories for FreeRate model (-cmin); no default.
vparam.specify_maxcat_ - (Integer) - Specify maximum number of categories for FreeRate model (-cmax); no default.
vparam.specify_merit_ - (String) - Specify either AIC, AICc or BIC for the optimality criterion (-merit); no default.
vparam.specify_fulltreesearch_ - (Switch) - Turn on full tree search for each model considered, to obtain more accurate result. (-mtree), no default.
vparam.specify_addlmodels_ - (String) - Specify a comma-separated list of mixture models to additionally consider for model selection. (-madd), no default.
Specify Substitution Models
vparam.freetextmodel_ - (String) - Specify any model as a free text string.
vparam.specify_dnamodel_ - (Excl) - Specify a DNA model (-m); JC69, F81, K80, HKY, TN93, TNe, K81, K81u, TPM2, TPM2u, TPM3, TPM3u, TIM, TIMe, TIM2, TIM2e, TIM3, TIM3e, TVM,TVMe, SYM, GTR; no default.
vparam.specify_protmodel_ - (Excl) Specify a Protein model (-m); BLOSUM62, cpREV, Dayhoff, DCMut, FLU, HIVb, HIVw, JTT, JTTDCMut, LG, mtART, mtMAM, mtREV, mtZOA, Poisson, PMB, rtREV, VT, WAG, C10, C20, C30, C40, C50, C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X, CF4; no default.
vparam.max_posteriormode_ - (Switch) Switch to posterior maximum mode for obtaining site-specific profiles (-fmax)
vparam.specify_binmodel_ - (Excl) - Specify a Binary/Morphological model (-m ) JC2, GTR2, MK, ORDERED; no default.
vparam.specify_codonmodel_ - (Excl) - Specify a Codon model (-m ); MG; MGK, MG1KTS, MG1KTV, MG2K, GY, GY1KTS, GY1KTV, GY2K, KOSI07, ECMrest, SCHN05; no def ault.
vparam.specify_modelfreq_ - (Excl) - Specify model frequency; +F, +FO, +FQ,+F1x4, +F3x4; no default.
vparam.optimize_weights_ - (Switch) - Turn on optimizing weights of mixture models (-mwopt)
vparam.specify_modelrate_ - (Excl) - Specify rate heterogeneity; +I, +G, +I+G, +R, +I+R; no default.
vparam.asc_bias_ - (Excl) - Correct for Ascertainment bias (+ASC); +ASC; no default.
vparam.gamma_shape_ - (Float) - Specify the Gamma shape parameter (-a); no default.
vparam.median_approximation_ - (Switch) - Perform the median approximation for Gamma rate heterogeneity (-gmedian); no default.
vparam.invariable_sites_ - (Float) quartSpecify the proportion of invariable sites; no default.
vparam.thorough_estimation_ - (Switch) - Perform more thorough estimation for +I+G model parameters (--opt-gamma-inv); no default.
Tree Search Parameters
vparam.slower_NNI_ - (Switch) - Turn on more thorough and slower NNI search (-allnni); no default.
vparam.no_mlpairwise_ - (Switch) Avoid computing ML pairwise distances and BIONJ tree (-djc)
vparam.use_fasttreesearch_ - (Switch) Turn on the fast tree search mode (-fast)
vparam.num_parstrees_ - (Integer) - Specify number of initial parsimony trees (-ninit); no default.
vparam.num_topparstrees_ - (Integer) - Specify number of top initial parsimony trees (-ntop); no detostopfault.
vparam.num_besttrees_ - (Integer) - Number of trees in the candidate set to maintain (-nbest))
vparam.num_unsucctostop_ - (Integer) - Number of unsuccessful iterations to stop (-nstop); no default.
vparam.perturb_strength_ - (Float) - Perturbation strength (between 0 and 1) (-pers)
vparam.num_tostop_ - (Integer) - Number of iterations to stop (-n); no default.
vparam.specify_radius_ - (Integer) - SPR radius for the initial search (-sprrad); default=6
vparam.perturb_strength_ - (Float) - Perturbation strength (between 0 and 1) (-pers); no default.
vparam.no_mlpairwise_ - (Switch) - Avoid computing ML pairwise distances and BIONJ tree (-djc); no default.
Bootstrap Search Parameters
vparam.bootstrap_type_ - (Excl) - Bootstrap Type; bb, b, bc; bo (no default)
vparam.num_bootreps_ - (Integer) - Specify number of bootstrap replicates (>=1000); no default.
vparam.write_boottrees_ - (Switch) - Turn on writing bootstrap trees to .ufboot file (-wbt); default=0.
vparam.write_boottrees1_ - (Switch) - Turn on writing bootstrap trees with branch lengths (-wbtl); default=0.
vparam.max_iters - (Integer) - Specify maximum number of iterations to stop. (-nm); default = 1000.
vparam.cc_ufboot_ - (Float) - Minimum correlation coefficient for UFBoot convergence criterion (-bcor); no default.
vparam.iter_interval_ - (Integer) - Iteration interval checking for UFBoot convergence (-nstep); no default.
vparam.specify_tiebreaker_ - (Float) - SPR radius for the initial search (-beps); no default.
vparam.part_resample_ - (Excl) - Resampling strategies for partitioned analysis (-bspec); GENE, GENESITE; no default.
Symmetry Tests
vparam.use_symmtest_ - (Switch) Run symmetry test(s) default=0
vparam.specify_symtest_ - (Excl) Symmetry Test; allowed values: symtest; symtest-remove-bad; symtest-remove-good; symtest-keep-zero no default.
vparam.specify_symtype_ - (Excl) When removing partitions, use: pval; MAR; INT default=pval
vparam.specify_pval_ - (Float) Specify a Symmetry p-value other than 0.05
Single Branch Tests
vparam.sh_test_ - (Switch) - SH-Like Test (-alrt); default=0.
vparam.parametrical_test_ - (Switch) Run the parametricaLRT test (-alrt 0) default=0
vparam.abayes_test_ - (Switch) - Approximate Bayes test (-abayes); default=0.
vparam.lbp_test_ - (Switch) - Fast local bootstrap probability (-lbp); default=0.
vparam.num_replicates_ - (Integer) - Specify number of replicates (1000 or less); no default.
Ancestral State Reconstruction
vparam.write_ancestralseqs_ - (Switch) Write ancestral sequences to .statefile (-asr)
vparam.specify_ancestralthresh_ - (Float) Specify minimum threshold of posterior probability for best ancestral state (-asr-min) no default
Tree Topology Tests
vparam.num_rell_ - (Integer) - Specify the number of RELL replicates (-zb)
vparam.weighted_tests_ - (Switch) - Perform the weighted-KH and weighted-SH tests; default=0.
vparam.unbiased_test_ - (Switch) - Perform the approximately unbiased (AU) test (-au); default=0.
vparam.estimate_parsetreeonly_ - (Switch) - Only estimate model parameters on an initial parsimony tree (-n 0)<
Consensus Trees
vparam.compute_consensustree_ - (Switch) - Compute consensus tree of the trees passed via -t (-con). default=0.
vparam.compute_consensusnetwork_ - (Switch) - Compute consensus network of the trees passed via -t; default=0.
vparam.min_threshold_ - (Float) - Specify a minimum threshold between 0 and 1 (-minsup); no default.
vparam.burnin_value_ - (Integer) - Specify a burn-in (-bi); no default.
vparam.overwrite_logs_ - (Switch) - Overwrite existing log files (default=0).
vparam.nodetarget_treefile_ - (String) - Specify name of a node in -sup target tree (-suptag); no default.
vparam.set_scalefactor_ - (String) Set the scaling factor of support values for -sup option (-scale)
vparam.set_precision_ - (String) Set the precision of support values for -sup option (-prec)
vparam.nodetarget_treefile_ - (String) Specify name of a node in -sup target tree (-suptag)
Computing Robinson's Foulds distances
vparam.compute_rfdistances_all_ - (Switch) - Compute all-to-all RF distances between all trees passed via -t (-rf_all); no default.
vparam.compute_rfdistances_adj_ - (Switch) - Compute RF distances between adjacent trees passed via -t (-rf_adj); no default.
Generate Random Trees
vparam.num_taxa_ - (Integer) Specify number of taxa for the tree (-r)
vparam.choose_randomtype_ - (Excl) Specify a model for the random tree; -r; -ru; -rcat; -rbal; -rcsg
vparam.specify_brlengths_ - (String) Specify minimum, mean and maximum branch lengths of the random tree DEFAULT:-rlen 0.001 0.1 0.999
vparam.specify_treefilename_ - (String) Specify a name for your random tree file (we recommend a name with .tree
Miscellaneous Options
vparam.per_sitefile_ - (Switch) - Write per-site rates to .rate file (-wsr) no default.
vparam.name_outfiles_ - (String) - Specify a prefix for the output files (--prefix)